As a result of recent advances in MEMS/NEMS and systems biology, as well as the emergence of synthetic bacteria and lab/process-on-a-chip technques, it is now possible to design chemical "circuits," custom organisms, micro/nanoscale swarms of devices, and a host of other new systems. This success opens up a new frontier for interdisciplinary communications techniques using chemistry, biology, and other principles that have not been considered in the communications literature.The IEEE Transactions on Molecular, Biological, and Multi-Scale Communications (T-MBMC) is devoted to the principles, design, and analysis of communication systems that use physics beyond classical electromagnetism. This includes molecular, quantum, and other physical, chemical and biological techniques; as well as new communication techniques at small scales or across multiple scales (e.g., nano to micro to macro; note that strictly nanoscale systems, 1-100 nm, are outside the scope of this journal). Original research articles on one or more of the following topics are within scope: mathematical modeling, information/communication and network theoretic analysis, standardization and industrial applications, and analytical or experimental studies on communication processes or networks in biology. Contributions on related topics may also be considered for publication. Contributions from researchers outside the IEEE’s typical audience are encouraged.

Inferring the structure and dynamics of network models is critical to understanding the functionality and control of complex systems, such as metabolic and regulatory biological networks. The increasing quality and quantity of experimental data enable statistical approaches based on information theory for model selection and goodness-of-fit metrics. We propose an alternative data-driven method to ...
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In this paper, we propose and investigate an estimate-and-forward (EF) relaying scheme with half-duplex transmission protocol in a two-hop diffusion-based molecular communication (DMC) system under the influence of both residual and counting noises. The proposed relaying scheme forwards an estimate of the transmitted number of molecules, which is derived using maximum likelihood principle. Based o...
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Information delivery using chemical molecules is an integral part of biology at multiple distance scales and has attracted recent interest in bioengineering and communication theory. Potential applications include cooperative networks with a large number of simple devices that could be randomly located (e.g., due to mobility). This paper presents the first tractable analytical model for the collec...
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In this paper, the error performance achieved by cooperative detection among K distributed receivers in a diffusion-based molecular communication (MC) system is analyzed and optimized. In this system, the receivers first make local hard decisions on the transmitted symbol and then report these decisions to a fusion center (FC). The FC combines the local hard decisions to make a global decision usi...
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We formulate an info-clustering paradigm based on a multivariate information measure, called multivariate mutual information, that naturally extends Shannon’s mutual information between two random variables to the multivariate case involving more than two random variables. With proper model reductions, we show that the paradigm can be applied to study the human genome and connectome in a mo...
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This paper provides the author's personal retrospective on molecular communication research. The author has been involved in molecular communication from its conceptualization to the establishment as a scientific discipline and its flourishing today. Based on his personal journey, the author describes the history of molecular communication research and shares what he learned from the journey. The ...
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We provide an overview of current approaches to DNA-based storage system design and of accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random access DNA storage channels. The analytic contribution of our work is the construction and design of sequences over discrete alphabets that avoid pre-specif...
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Diffusion-based molecular communication has become a promising scheme for communication between nanoscale devices, and various modulation schemes have recently been proposed, including type, quantity, and concentration modulation. In this paper, a novel approach of using both quantity and type of molecules to convey information is considered. An asynchronous threshold-based detection algorithm, ca...
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Molecular communications (MC) has been studied as a bio-inspired information carrier for micro-scale and nano-scale environments. On the macro-scale, it can also be considered as an alternative to electromagnetic (EM) wave based systems, especially in environments where there is significant attenuation to EM wave power. This paper goes beyond the unbounded free space propagation to examine three m...
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Advances in the field of synthetic biology have been key to demonstration of molecular computing systems in general and DNA in particular. This paper presents an overview of how continuous-time, discrete-time, and digital signal processing systems can be implemented using molecular reactions and DNA. In this paper, discrete-time systems refer to sampled signals with continuous signal amplitude. Si...
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Molecular communication (MC) is a communication strategy that uses molecules as carriers of information, and is widely used by biological cells. As an interdisciplinary topic, it has been studied by biologists, communication theorists and a growing number of information theorists. This paper aims to specifically bring MC to the attention of information theorists. To do this, we first highlight the...
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The aim of this paper is to model the “macroscopic” functioning of droplet-based microfluidic networks, i.e., the speed and trajectory of droplets across a network of microfluidic elements. To this end, we first give a quick overview of microfluidic basics and main governing rules. Based on such principles, we derive mathematical models of the fundamental components of a microfluidic...
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In this paper, we tackle the problem of how to locate a single entity with an unknown location in a vast underwater search space. In under-water channels, traditional wave-based signals suffer from rapid distance- and time-dependent energy attenuation, leading to expensive and lengthy search missions. In view of this, we investigate two molecular messaging methods for location discovery: 1) a Rose...
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In this paper, we present an analytical model for the diffusive molecular communication (MC) system with a reversible adsorption receiver in a fluid environment. The widely used concentration shift keying is considered for modulation. The time-varying spatial distribution of the information molecules under the reversible adsorption and desorption reaction at the surface of a receiver is analytical...
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In the nanonetworking literature, many solutions have been suggested to enable the nanomachine-to-nanomachine communication. Among these solutions, this paper focuses on what constitutes the basis for molecular communication paradigms- molecular communication via diffusion. In this paper, the channel for a spherical absorbing receiver under messenger molecule degradation is analytically modeled an...
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A molecular diffusion channel is a channel with memory, as molecules released into the medium hit the receptors after a random delay. Modulating over the diffusion channel is performed by choosing the type, intensity, or the released time of molecules diffused in the environment over time. Motivated by the desire to keep the encoder and decoder simple and the fact that channel state information is...
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This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular communication networks, bionanomachines, or biological cells, communicate with each other using a cell-to-cell communication mechanism mediated by a diffusible sign...
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In this paper, the capacity of a diffusion-based molecular communication network under the model of a Linear Time Invariant-Poisson (LTI-Poisson) channel is studied. Introduced in the context of molecular communication, the LTI-Poisson model is a natural extension of the conventional memoryless Poisson channel to include memory. Exploiting prior art on linear intersymbol interference (ISI) channel...
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As advances in nanotechnology continue their ascending course, new areas of application for nanoscale communication open up, involving biological systems. Such systems have peculiarities that must be taken into consideration, when trying to study new communication paradigms based on microbiological communication systems. In this paper, an innovative mathematical model is employed, in an effort to ...
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We propose a novel model of postsynaptic potential buildup and action potential upswing of cortical neurons using the generalized inverse Gaussian (GIG) diffusion of Barndorff-Nielsen, Blaesild, and Halgreen. A certain subset of GIG diffusions exhibit attraction to a threshold, a phenomenon widely observed in biological neurons. The parameters in this model control the variance, components of the ...
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The finite capacity of neural memory and the reconsolidation phenomenon suggest it is important to be able to update stored information as in a palimpsest, where new information overwrites old information. Moreover, changing information in memory is metabolically costly. In this paper, we suggest that information-theoretic approaches may inform the fundamental limits in constructi...
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In this paper, we consider a multi-hop molecular communication network consisting of one nanotransmitter, one nanoreceiver, and multiple nanotransceivers acting as relays. We consider three different relaying schemes to improve the range of diffusion-based molecular communication. In the first scheme, different types of messenger molecules are utilized in each hop of the multi-hop network. In the ...
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We propose a method to find optimal sparse connected approximations for large complex networks of nodes interacting over time. Optimality is measured by Kullback-Leibler divergence. The sparsity is controlled by the user through specifying the in-degrees. The approximations have spanning tree subgraphs, enabling them to depict flow through a network. They can also depict feedback. The approximatio...
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In a communication network with extremely high processing delays, an efficient addressing and multiple-access control mechanism to improve the throughput performance of the system is a necessity. This work focuses on source addressing in multiple-source, single-receiver bacterial communication networks. We propose Amplitude-Division Multiple Access (ADMA), a method that assigns the amplitude of th...
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One of the long-term goals of synthetic biology is to reliably engineer biological systems that perform human-defined functions such as sensing, monitoring, and processing. Molecular sensing via biological cells is often performed through receptors which interact with the signal molecules. The ligand receptors in bacteria are one of the most studied examples of such phenomenon. In this paper, we s...
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The computational capability of chemical reaction networks (CRNs) intensively motivates molecular computation. In this paper, a total of five systematic approaches of synthesizing combinational logic with chemical reactions are proposed. As in some of our earlier works, a Karnaugh map (K-map), which well depicts the logic function of a certain CRN system, is required for all approaches. Several co...
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Nanoscale communication is expected to offer unprecedented benefits. However, lack of a precise definition and general framework for nanoscale communication has resulted in limited impact and dissipated effort. The IEEE P1906.1/Draft 1.0 Recommended Practice for Nanoscale and Molecular Communication Framework provides the precise, common definition of nanoscale communication and a standard, genera...
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We provide a fundamental treatment of the molecular communication channel wherein “inscribed matter” is transmitted across a spatial gap to provide reliable signaling between a sender and receiver. Inscribed matter is defined as an ensemble of “tokens” (biotic/abiotic objects) and is inspired, at least partially, by biological systems where groups of individually constr...
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Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic analysis of the impact of insertion-deletion (indel) errors in nanopore sequencers. In particular, we consider the following problems: 1) for given indel error...
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Optimization results are one method for understanding neural computation from nature’s perspective and for defining the physical limits on neuron-like engineering. Earlier work looks at individual properties or performance criteria and occasionally a combination of two, such as energy and information. Here, as the optimization method, we make use of Jaynes’ maximum entropy method and...
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Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate real-time data about their environmental conditions, but the biochemical reaction networks that propagate, amplify, and process signals work with noisy representations of that data. Biology must implement strategies that not only filter the noise b...
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Understanding and even defining what constitutes animal interactions remains a challenging problem. Correlational tools may be inappropriate for detecting communication between a set of many agents exhibiting nonlinear behavior. A different approach is to define coordinated motions in terms of an information theoretic channel of direct causal information flow. In this work, we consider time series...
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Claude Shannon’s information theory has been applied to neural information transmission and information rates of up to hundreds of bits per second have been estimated for single spiking neurons. For Gaussian white-noise signals, one can meaningfully resolve the single number of information rate with respect to frequencies and pose the corresponding question: does a neuron encode information...
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An adaptive control method of angular sensitivity for a VHF-band nano-antenna is presented. This antenna is composed of a single carbon nanotube cantilever immersed in a DC electric field. The behavior of the antenna is analytically described using a singly clamped metallic sphere model and the image charge method. We derive design guidelines for the direction and shape of angular sensitivity; the...
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In this paper, we consider bacterial point-to-point and multiple-access molecular communications with ligand-receptors. For point-to-point communication, we investigate common signaling methods, namely, the level scenario, in which the information is encoded into multiple concentration levels of a single molecule type, and the type scenario, in which the information bits are encoded in multiple mo...
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One of the major bottlenecks in nanonetworks is the very limited energy that can be accessed by nanodevices. To achieve perpetual data transmission, it is required to investigate in-depth the relationship between energy harvesting and consumption, and the underlying constraints in nanonetworks. In this paper, the tradeoff between energy harvesting and consumption is analyzed by considering the pec...
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Molecular communication via diffusion (MCvD) is a new field of communication where molecules are used to transfer information. One of the main challenges in MCvD is the intersymbol interference (ISI), which inhibits communication at high data rates. Furthermore, at nanoscale, energy efficiency becomes an essential problem. Before addressing these problems, a predetermined threshold for the receive...
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The communication efficiency between a transmitter and a receiver is affected by motion and the presence of gravitational fields. We study the effect of regenerating the signal in intermediate repeaters in different relativistic scenarios where relativistic effects on communication can become relevant, like ships moving at relativistic speeds or in the proximity of black holes. Without any repeate...
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This paper quantifies a molecular measurement system as it may be applied to real-time brain activity mapping. The network's signal source consists of biologically synthesized molecular recorders embedded in each neuron. This means of measurement promises the ability to obtain unprecedented levels of operational brain detail, but poses a formidable challenge in communicating its recordings outside...
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Cells must make decisions based on noisy measurements of their environment. One way for cells to manage this noise is to attempt to minimize its effect. However, this may not always be possible, or may prove to be costly. On the other hand, the noise may be managed so that the correct decision is made most of the time. Shannon introduced rate distortion theory to evaluate the efficiency of systems...
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This paper examines the information transmission capacity of a high-density protein microarray based on an equivalent model of a multi-analyte molecular communication system. The capacity of the microarray is computed by taking into account the performance limiting factors such as channel diffusion characteristics, the channel noise and the saturation properties of the receptor probes. Our modelin...
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A genomic symbol to signal conversion concept is introduced and demonstrated on nucleotide base pairs and amino acid codons. Binary encodings of the presence or absence of bioinformatic attributes (e.g., physical, chemical, functional, structural, etc.) onto Euclidean signal space points of +1 or -1 is performed for individual base pairs or blocks of DNA symbols such as amino acid codons. The symb...
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Motivated by recent discoveries of microbial communities that transfer electrons across centimeter-length scales, this paper studies the information capacity of bacterial cables via electron transfer, which coexists with molecular diffusion, under the assumption of full causal channel state information (CSI). The bacterial cable is modeled as an electron queue that transfers electrons from the enc...
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In contrast to second-generation DNA sequencing technologies, emerging third-generation technologies are capable of delivering reads that are long enough to enable perfect genome assembly. Unfortunately, the benefits of long reads are accompanied by higher rates of read errors. This motivates a question of fundamental import: what read-length and error-rate combinations allow for perfect assembly ...
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The design and analysis of diffusive molecular communication systems generally requires knowledge of the environment's physical and chemical properties. Furthermore, prospective applications might rely on the timely detection of changes in the local system parameters. This paper studies the local estimation of channel parameters for diffusive molecular communication when a transmitter releases mol...
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Bioinspired communication techniques are emerging with increasing interest in parallel with recent advancements of nanotechnology. Particular interest is observed in the development of neuronal interfaces for human-machine communication and nanoscale neuronal devices. We propose a novel description of the communication pathways existing in the neuronal circuits, based on the abstract dynamics betw...
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In this paper, electroencephalography (EEG) measurements are used to infer change in cortical functional connectivity in response to change in audio stimulus. Experiments are conducted wherein the EEG activity of human subjects is recorded as they listen to audio sequences whose quality varies with time. A causal information theoretic framework is then proposed to measure the information flow betw...
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In this paper, a mesoscopic-to-observable dynamic model of the pore formation measurement platform is presented. The platform is composed of a controllable engineered tethered membrane. Using the mesoscopic-to-observable model and experimental measurements allows the platform to be used to gain insight into the pore formation dynamics of peptides in biological membranes. These results are useful f...
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Aims & Scope

As a result of recent advances in MEMS/NEMS and systems biology, as well as the emergence of synthetic bacteria and lab/process-on-a-chip technques, it is now possible to design chemical "circuits," custom organisms, micro/nanoscale swarms of devices, and a host of other new systems. This success opens up a new frontier for interdisciplinary communications techniques using chemistry, biology, and other principles that have not been considered in the communications literature.The IEEE Transactions on Molecular, Biological, and Multi-Scale Communications (T-MBMC) is devoted to the principles, design, and analysis of communication systems that use physics beyond classical electromagnetism. This includes molecular, quantum, and other physical, chemical and biological techniques; as well as new communication techniques at small scales or across multiple scales (e.g., nano to micro to macro; note that strictly nanoscale systems, 1-100 nm, are outside the scope of this journal). Original research articles on one or more of the following topics are within scope: mathematical modeling, information/communication and network theoretic analysis, standardization and industrial applications, and analytical or experimental studies on communication processes or networks in biology. Contributions on related topics may also be considered for publication. Contributions from researchers outside the IEEE’s typical audience are encouraged.

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Aims & Scope

As a result of recent advances in MEMS/NEMS and systems biology, as well as the emergence of synthetic bacteria and lab/process-on-a-chip techniques, it is now possible to design chemical “circuits”, custom organisms, micro/nanoscale swarms of devices, and a host of other new systems. This success opens up a new frontier for interdisciplinary communications techniques using chemistry, biology, and other principles that have not been considered in the communications literature. The IEEE Transactions on Molecular, Biological, and Multi-Scale Communications (T-MBMSC) is devoted to the principles, design, and analysis of communication systems that use physics beyond classical electromagnetism. This includes molecular, quantum, and other physical, chemical and biological techniques; as well as new communication techniques at small scales or across multiple scales (e.g., nano to micro to macro; note that strictly nanoscale systems, 1-100 nm, are outside the scope of this journal). Original research articles on one or more of the following topics are within scope: mathematical modeling, information/communication and network theoretic analysis, standardization and industrial applications, and analytical or experimental studies on communication processes or networks in biology. Contributions on related topics may also be considered for publication. Contributions from researchers outside the IEEE’s typical audience are encouraged.